Ligand profile

PMN

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_31484 — 3-oxoacyl-[acyl-carrier-protein] synthase 2

Via homolog PDB 2gfx UniProt P0AAI5 Formula C₂₄H₂₇NO₇
Mol. weight 441.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PMN
PDB
2gfx
UniProt (similar protein)
P0AAI5
Target protein
KP13_31484

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 441.48 Da
LogP (Crippen) 3.23
H-bond donors 4
H-bond acceptors 6
TPSA 133.16 Ų
Rotatable bonds 5
Aromatic rings 1 / 6
Heavy atoms 32
Fraction sp³ C 0.54
Formula C₂₄H₂₇NO₇

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 133.2
  • −1 ≤ LogP ≤ 5 3.23
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 441.5
  • LogP ≤ 5 3.23
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 133.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@]12C[C@]34C[C@H]1C[C@@H]([C@H]3[C@](C(=O)C=C4)(C)CCC(=O)Nc5c(ccc(c5O)C(=O)O)O)O2
InChI 
InChI=1S/C24H27NO7/c1-22(7-6-17(28)25-18-14(26)4-3-13(19(18)29)21(30)31)16(27)5-8-24-10-12-9-15(20(22)24)32-23(12,2)11-24/h3-5,8,12,15,20,26,29H,6-7,9-11H2,1-2H3,(H,25,28)(H,30,31)/t12-,15+,20+,22-,23+,24+/m1/s1
InChIKey 
CSOMAHTTWTVBFL-OFBLZTNGSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF00109' 'PF02801

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_31484.

PDB 12

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 15

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)